How do I use SPADE?

High-dimensional single-cell technologies, such as Flow, Mass and Image cytometry, can measure dozens of parameters at the single-cell level. FCS Express integrates Spanning-tree Progression Analysis of Density-normalized Events, otherwise known as SPADE, which is a tool that extracts a hierarchy from high-dimensional cytometry data in an unsupervised manner and allows users to visualize multiple cell types in a branched tree structure without requiring the user to define a known cellular ordering.

The final result of the algorithm in FCS Express is a Heat Map plot in which each cell type is depicted as a node of the branched tree. The Heat Map plot can be formatted to color each node based on the expression of a given marker. Moreover, the size of each node can be made proportional to a given statistic (e.g., the number of events within the node).

Gates may be defined on SPADE transformed Heat Map plot to select one or multiple nodes for downstream analysis. Similarly, gates created on classical dot plots can be applied to SPADE plots as well.

Learn more about using SPADE via the FCS Express Manual at:

SPADE (Spanning-tree Progression Analysis of Density-normalized Events) is a clustering algorithm. Its goal is to automatically identify cell populations in multidimensional cytometry data files. FCS Express 6 and later allows users to run SPADE on Flow, Mass and Image cytometry data.

More details on SPADE can be found in the following publications:

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